Your diagnosis

Celiac disease

This article will help you read and understand your pathology report for celiac disease.

by Shaheed Hakim, MD FRCPC, updated December 11, 2020

Quick facts:
  • Celiac disease is a condition that develops in people who have a sensitivity to gluten.
  • Gluten causes the immune system to damage the cells on the inside of the small intestine.
  • The damaged small intestine cannot absorb nutrients which can lead to weight loss and diarrhea.
  • When examined under a microscope, the tissue from the small bowel will show a loss of villi and increased lymphocytes.

The function and anatomy of the small bowel

The small bowel is a part of the digestive system. Another name for the small bowel is the small intestine. The small bowel is a long tube that starts at the stomach and ends at the colon. It is divided into three parts: duodenum, jejunum, and ileum. The duodenum is the shortest part of the small bowel. It connects to the stomach on the right side of the body just below the ribs.

Food that we eat enters the stomach where it is mixed and broken down by strong acids made by cells inside the stomach. When this is complete, the digested food moves into the small bowel. The purpose of the small bowel is to absorb nutrients from the food and transport those nutrients into the body.

The inside of the duodenum is lined by epithelial cells that are specially designed to absorb nutrients from the food we eat. These specialized cells form a barrier called an epithelium. Below the epithelium is a thin layer of tissue called the lamina propria. This tissue contains many small blood vessels which support the epithelial cells.

duodenum normal

Mucosa is a word pathologists use to describe the epithelium and lamina propria together. The mucosa in the small bowel grows in a way that creates long finger-like projections of tissue called villi. These villi allow the small bowel to have a large surface area in a relatively small space.

Below the mucosa are specialized cells that connect to form round structures called Brunner’s glands. These glands produce substances which protect the epithelial cells from the strong acid coming from the stomach.


Gluten is a small molecule that is naturally found in wheat, rye, and barely. As a result, many foods such as baked goods, pastas, noodles, cereals, sauces, and alcoholic beverages contain gluten. Gluten is normally broken down in the gastrointestinal tract into smaller parts which are then absorbed by the body.

What is Celiac disease?

Celiac disease is a medical condition that develops when the body reacts abnormally to the gluten found in food. The abnormal reaction damages the cells on the inside of the small intestine. Another name for celiac disease is gluten sensitive enteropathy.

This irritation causes small immune cells called lymphocytes to enter the space between the epithelial cells in the epithelium. Pathologists refer to this as increased intraepithelial lymphocytes.

Overtime, these immune cells damage the epithelium which causes a loss of the normal villi. Pathologists describe this change as atrophy or blunting of the villi.

How do pathologists make this diagnosis?

A biopsy is usually performed because the patient has symptoms suggestive of celiac disease (gluten sensitive enteropathy), which may include weakness and diarrhea. These symptoms occur when the patient eats food that contain gluten.  Biopsies are usually taken from the 2nd part of the duodenum, where the changes associated with celiac disease are easiest to recognize.

A diagnosis of celiac disease (gluten sensitive enteropathy) requires both clinical and pathological confirmation. Clinical confirmation is usually made by performing blood tests for antibodies that target tissue transglutaminase. These antibodies are found in most patients with celiac disease. Pathological confirmation is made after a biopsy is examined by a pathologist.

Your pathologist can confirm the diagnosis when they see increased intraepithelial lymphocytes in the epithelium of the small intestine, as well as the abnormal blunting or atrophy of the villi.  This blunting can further be graded as mild, moderate or severe. In severe blunting there are no villi seen and the epithelium looks flat.

Increased intraepithelial lymphocytes with no/mild villous blunting

When a tissue sample is taken from the duodenum in the early stages of the disease, the small intestine may show only mild changes including an increased number of lymphocytes in the epithelium on the inner surface of the tissue. In many early cases, the villi are still normal and the report will refer to this as ‘no or mild villous blunting’.

The finding of increased intraepithelial lymphocytes without villous blunting is not unique to Celiac disease and may be seen in other conditions. For example, Helicobacter gastroenteritis, medications (ie. Olmesartan), tropical sprue, protein intolerance, bacterial overgrowth and viral gastroenteritis all cause changes that look similar under the microscope.


Dysplasia refers to an abnormal pattern of growth that is initially non-cancerous but can turn into cancer. Chronic inflammation can lead to dysplasia.

The earliest change is referred to as low grade dysplasia.  The cells in low grade dysplasia are abnormal but are still non-cancerous. In some cases, the cells become even more abnormal and progress to high grade dysplasia. These cells look very similar to cancer cells, however, they are still only seen in the epithelium on the inner surface of the stomach.

High grade dysplasia is considered a pre-cancerous condition because it is associated with an increased risk of developing cancer in the small intestine over time. Your pathologist will closely examine the tissue for any evidence of dysplasia and will describe it in your report if it is seen.

Enteropathy-associated T-cell lymphoma (EATL)

In some patients, a gluten free diet is not enough to prevent inflammation and damage in the small intestine.  These patients are classified as having refractory celiac disease. In a specific type of refractory celiac disease, the inflammatory cells (intraepithelial lymphocytes) divide and multiply in an abnormal pattern.  This leads to a cancer called enteropathy-associated T-cell lymphoma (EATL), a type of lymphoma.

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